NOTE: Most plots are interactive and you can use the legend to specify samples/treatment of interest. You can also download an .svg version of each figure within this report.


  Pre- and Post-Adapter Removal Read Stats




Total number of reads before and after adapter removal


Forward (R1) and reverse (R2) read length before and after adapter removal




  Number of Reads Per Sample









  Rarefaction






  Diversity Analyses Plots



Shannon diversty


## [1] "Shapiro Test of normality - data is normal p-value > 0.05"
##
##  Shapiro-Wilk normality test
##
## data:  resid(shannonaov)
## W = 0.9291, p-value = 0.5732
##
##
## --------------------------------------------------------------
##
## [1] "Bartlett Test variance homogeneity - variance is homogeneous p-value > 0.05"
##
##  Bartlett test of homogeneity of variances
##
## data:  index by treatment
## Bartlett's K-squared = 1.0859, df = 1, p-value = 0.2974
##
##
## --------------------------------------------------------------
##
## [1] "ANOVA Results"
##             Df Sum Sq Mean Sq F value Pr(>F)
## treatment    1 0.0527  0.0527    0.15  0.718
## Residuals    4 1.4061  0.3515
##
## --------------------------------------------------------------
##
## [1] "Tukey HSD - Pairwise comparison - significant differences indicated by p-value < 0.05"
##   Tukey multiple comparisons of means
##     95% family-wise confidence level
##
## Fit: aov(formula = index ~ treatment, data = shannondata5_2)
##
## $treatment
##                     diff       lwr     upr     p adj
## Group2-Group1 -0.1874213 -1.531512 1.15667 0.7183604
##
##
## --------------------------------------------------------------





Simpson diversty


## [1] "Shapiro Test of normality - data is normal p-value > 0.05"
##
##  Shapiro-Wilk normality test
##
## data:  resid(simpsonaov)
## W = 0.88738, p-value = 0.3047
##
##
## --------------------------------------------------------------
##
## [1] "Bartlett Test variance homogeneity - variance is homogeneous p-value > 0.05"
##
##  Bartlett test of homogeneity of variances
##
## data:  index by treatment
## Bartlett's K-squared = 0.74903, df = 1, p-value = 0.3868
##
##
## --------------------------------------------------------------
##
## [1] "ANOVA Results"
##             Df Sum Sq Mean Sq F value Pr(>F)
## treatment    1 0.0052 0.00519   0.059   0.82
## Residuals    4 0.3506 0.08764
##
## --------------------------------------------------------------
##
## [1] "Tukey HSD - Pairwise comparison - significant differences indicated by p-value < 0.05"
##   Tukey multiple comparisons of means
##     95% family-wise confidence level
##
## Fit: aov(formula = index ~ treatment, data = simpsondata5_2)
##
## $treatment
##                      diff        lwr       upr     p adj
## Group2-Group1 -0.05883652 -0.7299494 0.6122763 0.8196598
##
##
## --------------------------------------------------------------





Species Richness


## [1] "Shapiro Test of normality - data is normal p-value > 0.05"
##
##  Shapiro-Wilk normality test
##
## data:  resid(richaov)
## W = 0.93289, p-value = 0.6026
##
##
## --------------------------------------------------------------
##
## [1] "Bartlett Test variance homogeneity - variance is homogeneous p-value > 0.05"
##
##  Bartlett test of homogeneity of variances
##
## data:  index by treatment
## Bartlett's K-squared = 3.2991, df = 1, p-value = 0.06932
##
##
## --------------------------------------------------------------
##
## [1] "ANOVA Results"
##             Df Sum Sq Mean Sq F value Pr(>F)
## treatment    1  7.288   7.288   1.561   0.28
## Residuals    4 18.670   4.667
##
## --------------------------------------------------------------
##
## [1] "Tukey HSD - Pairwise comparison - significant differences indicated by p-value < 0.05"
##   Tukey multiple comparisons of means
##     95% family-wise confidence level
##
## Fit: aov(formula = index ~ treatment, data = richdata5_2)
##
## $treatment
##                   diff       lwr      upr     p adj
## Group2-Group1 2.204189 -2.693449 7.101827 0.2795884
##
##
## --------------------------------------------------------------






  Distance To Centroid 


##
## Call:
## adonis(formula = bray.distance ~ data5$treatment)
##
## Permutation: free
## Number of permutations: 719
##
## Terms added sequentially (first to last)
##
##                 Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)
## data5$treatment  1   1.01309 1.01309  4.6942 0.53992    0.1
## Residuals        4   0.86326 0.21582         0.46008
## Total            5   1.87635                 1.00000






  NMDS Plots


2D NMDS


## Run 0 stress 4.35166e-05
## Run 1 stress 9.206128e-05
## ... Procrustes: rmse 0.2192141  max resid 0.4447335
## Run 2 stress 0
## ... New best solution
## ... Procrustes: rmse 0.1475603  max resid 0.2719593
## Run 3 stress 0.1967694
## Run 4 stress 0
## ... Procrustes: rmse 0.1503594  max resid 0.2805032
## Run 5 stress 0
## ... Procrustes: rmse 0.1890022  max resid 0.2367295
## Run 6 stress 0
## ... Procrustes: rmse 0.1525354  max resid 0.2259206
## Run 7 stress 0
## ... Procrustes: rmse 0.1446005  max resid 0.2074821
## Run 8 stress 0
## ... Procrustes: rmse 0.132074  max resid 0.2500861
## Run 9 stress 0
## ... Procrustes: rmse 0.1888654  max resid 0.3103119
## Run 10 stress 0
## ... Procrustes: rmse 0.1321098  max resid 0.2335853
## Run 11 stress 0
## ... Procrustes: rmse 0.1086904  max resid 0.198957
## Run 12 stress 0
## ... Procrustes: rmse 0.184796  max resid 0.2895882
## Run 13 stress 0
## ... Procrustes: rmse 0.1985743  max resid 0.2828424
## Run 14 stress 0
## ... Procrustes: rmse 0.1839276  max resid 0.339448
## Run 15 stress 0
## ... Procrustes: rmse 0.1569956  max resid 0.2738898
## Run 16 stress 0
## ... Procrustes: rmse 0.08147595  max resid 0.1293814
## Run 17 stress 0
## ... Procrustes: rmse 0.1231843  max resid 0.1929613
## Run 18 stress 0
## ... Procrustes: rmse 0.2154224  max resid 0.3725087
## Run 19 stress 0
## ... Procrustes: rmse 0.09658586  max resid 0.169947
## Run 20 stress 0
## ... Procrustes: rmse 0.1123304  max resid 0.1810664
## Run 21 stress 0
## ... Procrustes: rmse 0.07114148  max resid 0.08562701
## Run 22 stress 0
## ... Procrustes: rmse 0.1207696  max resid 0.2088403
## Run 23 stress 0
## ... Procrustes: rmse 0.1338395  max resid 0.2011499
## Run 24 stress 0
## ... Procrustes: rmse 0.2011198  max resid 0.2879716
## Run 25 stress 7.960692e-05
## ... Procrustes: rmse 0.1835879  max resid 0.3361377
## Run 26 stress 7.465245e-05
## ... Procrustes: rmse 0.1516833  max resid 0.21161
## Run 27 stress 4.134366e-05
## ... Procrustes: rmse 0.158652  max resid 0.1955455
## Run 28 stress 9.401493e-05
## ... Procrustes: rmse 0.1705531  max resid 0.3146807
## Run 29 stress 0
## ... Procrustes: rmse 0.140281  max resid 0.1899751
## Run 30 stress 0
## ... Procrustes: rmse 0.1569951  max resid 0.237474
## Run 31 stress 0
## ... Procrustes: rmse 0.21383  max resid 0.3404873
## Run 32 stress 0
## ... Procrustes: rmse 0.1831665  max resid 0.2903409
## Run 33 stress 0
## ... Procrustes: rmse 0.1862874  max resid 0.2430944
## Run 34 stress 0
## ... Procrustes: rmse 0.1398732  max resid 0.194408
## Run 35 stress 0
## ... Procrustes: rmse 0.08385465  max resid 0.1208572
## Run 36 stress 0
## ... Procrustes: rmse 0.1531769  max resid 0.2654934
## Run 37 stress 0.1420473
## Run 38 stress 0
## ... Procrustes: rmse 0.168821  max resid 0.2760271
## Run 39 stress 0
## ... Procrustes: rmse 0.2398039  max resid 0.4101748
## Run 40 stress 4.958545e-05
## ... Procrustes: rmse 0.1690092  max resid 0.224612
## Run 41 stress 0
## ... Procrustes: rmse 0.1763536  max resid 0.2979007
## Run 42 stress 8.50985e-05
## ... Procrustes: rmse 0.2037257  max resid 0.3652396
## Run 43 stress 0
## ... Procrustes: rmse 0.1373896  max resid 0.1978843
## Run 44 stress 0
## ... Procrustes: rmse 0.1721457  max resid 0.2384637
## Run 45 stress 8.338233e-06
## ... Procrustes: rmse 0.1350539  max resid 0.1826055
## Run 46 stress 8.733644e-05
## ... Procrustes: rmse 0.1864883  max resid 0.2843063
## Run 47 stress 0
## ... Procrustes: rmse 0.1287125  max resid 0.1800035
## Run 48 stress 1.294414e-05
## ... Procrustes: rmse 0.06488975  max resid 0.09540012
## Run 49 stress 0
## ... Procrustes: rmse 0.1123794  max resid 0.2193415
## Run 50 stress 0
## ... Procrustes: rmse 0.0873931  max resid 0.1388494
## Run 51 stress 0
## ... Procrustes: rmse 0.1836172  max resid 0.2892836
## Run 52 stress 0
## ... Procrustes: rmse 0.1349277  max resid 0.2496178
## Run 53 stress 0
## ... Procrustes: rmse 0.1597566  max resid 0.3010393
## Run 54 stress 0
## ... Procrustes: rmse 0.1578135  max resid 0.2739341
## Run 55 stress 0.1420473
## Run 56 stress 9.580941e-05
## ... Procrustes: rmse 0.2385671  max resid 0.3099702
## Run 57 stress 0
## ... Procrustes: rmse 0.1424363  max resid 0.203378
## Run 58 stress 0
## ... Procrustes: rmse 0.1498625  max resid 0.2312135
## Run 59 stress 0
## ... Procrustes: rmse 0.08465851  max resid 0.1346232
## Run 60 stress 0
## ... Procrustes: rmse 0.1430299  max resid 0.2610707
## Run 61 stress 0
## ... Procrustes: rmse 0.1369128  max resid 0.1816959
## Run 62 stress 0
## ... Procrustes: rmse 0.08119163  max resid 0.1444967
## Run 63 stress 0
## ... Procrustes: rmse 0.1710694  max resid 0.240634
## Run 64 stress 9.84601e-05
## ... Procrustes: rmse 0.1878078  max resid 0.2714905
## Run 65 stress 0
## ... Procrustes: rmse 0.05651144  max resid 0.09672819
## Run 66 stress 8.62831e-05
## ... Procrustes: rmse 0.0727498  max resid 0.09722458
## Run 67 stress 0
## ... Procrustes: rmse 0.1958305  max resid 0.2910121
## Run 68 stress 2.701363e-05
## ... Procrustes: rmse 0.2225825  max resid 0.3507306
## Run 69 stress 7.042554e-05
## ... Procrustes: rmse 0.173566  max resid 0.2626667
## Run 70 stress 2.745518e-05
## ... Procrustes: rmse 0.08284383  max resid 0.124135
## Run 71 stress 0
## ... Procrustes: rmse 0.1840454  max resid 0.3503948
## Run 72 stress 0
## ... Procrustes: rmse 0.1540941  max resid 0.2302387
## Run 73 stress 0
## ... Procrustes: rmse 0.07616243  max resid 0.1113843
## Run 74 stress 0
## ... Procrustes: rmse 0.1348955  max resid 0.2398141
## Run 75 stress 0
## ... Procrustes: rmse 0.1593818  max resid 0.2624199
## Run 76 stress 0
## ... Procrustes: rmse 0.1658679  max resid 0.2368498
## Run 77 stress 0
## ... Procrustes: rmse 0.1083634  max resid 0.1355875
## Run 78 stress 0
## ... Procrustes: rmse 0.173316  max resid 0.2188972
## Run 79 stress 2.412692e-05
## ... Procrustes: rmse 0.1513869  max resid 0.2559945
## Run 80 stress 0
## ... Procrustes: rmse 0.1286293  max resid 0.1708846
## Run 81 stress 8.249084e-05
## ... Procrustes: rmse 0.1600543  max resid 0.2790534
## Run 82 stress 0
## ... Procrustes: rmse 0.06425533  max resid 0.09782641
## Run 83 stress 0
## ... Procrustes: rmse 0.1859754  max resid 0.3306764
## Run 84 stress 1.218079e-05
## ... Procrustes: rmse 0.1579732  max resid 0.2679705
## Run 85 stress 0
## ... Procrustes: rmse 0.1373995  max resid 0.1704452
## Run 86 stress 0
## ... Procrustes: rmse 0.1135352  max resid 0.1456319
## Run 87 stress 3.345478e-06
## ... Procrustes: rmse 0.1136627  max resid 0.1526098
## Run 88 stress 7.30298e-05
## ... Procrustes: rmse 0.09087387  max resid 0.1523526
## Run 89 stress 0
## ... Procrustes: rmse 0.1294085  max resid 0.20968
## Run 90 stress 0
## ... Procrustes: rmse 0.2133609  max resid 0.307295
## Run 91 stress 0
## ... Procrustes: rmse 0.208796  max resid 0.3331994
## *** No convergence -- monoMDS stopping criteria:
##     88: stress < smin
##      1: stress ratio > sratmax
##      2: scale factor of the gradient < sfgrmin
## [1] "No Convergence"





3D NMDS


## Run 0 stress 9.179259e-05
## Run 1 stress 0
## ... New best solution
## ... Procrustes: rmse 0.1912644  max resid 0.3064663
## Run 2 stress 0
## ... Procrustes: rmse 0.1515697  max resid 0.1940969
## Run 3 stress 8.011522e-05
## ... Procrustes: rmse 0.2408658  max resid 0.3233412
## Run 4 stress 0
## ... Procrustes: rmse 0.1502567  max resid 0.2373834
## Run 5 stress 0
## ... Procrustes: rmse 0.1824273  max resid 0.2309358
## Run 6 stress 0
## ... Procrustes: rmse 0.2044446  max resid 0.3064849
## Run 7 stress 0
## ... Procrustes: rmse 0.1360824  max resid 0.1868316
## Run 8 stress 0
## ... Procrustes: rmse 0.224697  max resid 0.3889081
## Run 9 stress 1.601269e-06
## ... Procrustes: rmse 0.2017323  max resid 0.253622
## Run 10 stress 0
## ... Procrustes: rmse 0.2332277  max resid 0.2830118
## Run 11 stress 0
## ... Procrustes: rmse 0.2094351  max resid 0.3393129
## Run 12 stress 0
## ... Procrustes: rmse 0.1924744  max resid 0.2476726
## Run 13 stress 0
## ... Procrustes: rmse 0.1723438  max resid 0.2779048
## Run 14 stress 0
## ... Procrustes: rmse 0.231938  max resid 0.3082758
## Run 15 stress 0
## ... Procrustes: rmse 0.1591339  max resid 0.2941593
## Run 16 stress 1.844663e-05
## ... Procrustes: rmse 0.1367305  max resid 0.1893536
## Run 17 stress 0
## ... Procrustes: rmse 0.2432104  max resid 0.3742779
## Run 18 stress 0
## ... Procrustes: rmse 0.2021536  max resid 0.3190184
## Run 19 stress 8.261138e-05
## ... Procrustes: rmse 0.2661264  max resid 0.3395278
## Run 20 stress 0
## ... Procrustes: rmse 0.2050021  max resid 0.3470228
## Run 21 stress 0
## ... Procrustes: rmse 0.2349675  max resid 0.3899205
## Run 22 stress 0
## ... Procrustes: rmse 0.1743172  max resid 0.3327414
## Run 23 stress 0
## ... Procrustes: rmse 0.1805854  max resid 0.2484891
## Run 24 stress 0
## ... Procrustes: rmse 0.2214565  max resid 0.3735158
## Run 25 stress 6.602248e-05
## ... Procrustes: rmse 0.2633094  max resid 0.3328158
## Run 26 stress 0
## ... Procrustes: rmse 0.1989565  max resid 0.3402747
## Run 27 stress 0
## ... Procrustes: rmse 0.2434265  max resid 0.2853429
## Run 28 stress 0
## ... Procrustes: rmse 0.1437204  max resid 0.2008141
## Run 29 stress 0
## ... Procrustes: rmse 0.2207409  max resid 0.2922027
## Run 30 stress 0
## ... Procrustes: rmse 0.140996  max resid 0.2320052
## Run 31 stress 0
## ... Procrustes: rmse 0.1889331  max resid 0.2900138
## Run 32 stress 0
## ... Procrustes: rmse 0.1834047  max resid 0.2422162
## Run 33 stress 0
## ... Procrustes: rmse 0.2447367  max resid 0.3580808
## Run 34 stress 0
## ... Procrustes: rmse 0.2359379  max resid 0.3172238
## Run 35 stress 0
## ... Procrustes: rmse 0.2428633  max resid 0.3027342
## Run 36 stress 0
## ... Procrustes: rmse 0.2011346  max resid 0.344021
## Run 37 stress 0
## ... Procrustes: rmse 0.2398276  max resid 0.4186627
## Run 38 stress 6.012963e-05
## ... Procrustes: rmse 0.2290966  max resid 0.3002383
## Run 39 stress 0
## ... Procrustes: rmse 0.2681661  max resid 0.4893852
## Run 40 stress 2.102041e-05
## ... Procrustes: rmse 0.1696101  max resid 0.2438495
## Run 41 stress 0
## ... Procrustes: rmse 0.2461656  max resid 0.3874782
## Run 42 stress 8.813298e-05
## ... Procrustes: rmse 0.2458929  max resid 0.3572947
## Run 43 stress 1.301719e-06
## ... Procrustes: rmse 0.196147  max resid 0.322213
## Run 44 stress 0
## ... Procrustes: rmse 0.1521486  max resid 0.2327491
## Run 45 stress 7.430631e-05
## ... Procrustes: rmse 0.2806763  max resid 0.3795962
## Run 46 stress 0
## ... Procrustes: rmse 0.1268192  max resid 0.1828082
## Run 47 stress 0
## ... Procrustes: rmse 0.1656652  max resid 0.2345423
## Run 48 stress 0
## ... Procrustes: rmse 0.2071554  max resid 0.3748716
## Run 49 stress 8.899945e-05
## ... Procrustes: rmse 0.2411995  max resid 0.3239697
## Run 50 stress 8.49387e-05
## ... Procrustes: rmse 0.2235364  max resid 0.2957555
## Run 51 stress 8.946254e-05
## ... Procrustes: rmse 0.2411916  max resid 0.3239556
## Run 52 stress 0
## ... Procrustes: rmse 0.1024931  max resid 0.1772733
## Run 53 stress 0
## ... Procrustes: rmse 0.1805318  max resid 0.2266111
## Run 54 stress 0
## ... Procrustes: rmse 0.222073  max resid 0.3309312
## Run 55 stress 0
## ... Procrustes: rmse 0.1984136  max resid 0.2676206
## Run 56 stress 4.061045e-05
## ... Procrustes: rmse 0.1650274  max resid 0.2850801
## Run 57 stress 0
## ... Procrustes: rmse 0.2278851  max resid 0.350922
## Run 58 stress 0
## ... Procrustes: rmse 0.1401086  max resid 0.185101
## Run 59 stress 8.737338e-05
## ... Procrustes: rmse 0.2411935  max resid 0.3239583
## Run 60 stress 0
## ... Procrustes: rmse 0.2191345  max resid 0.3940798
## Run 61 stress 2.198444e-05
## ... Procrustes: rmse 0.2350082  max resid 0.3891647
## Run 62 stress 0
## ... Procrustes: rmse 0.2048775  max resid 0.265205
## Run 63 stress 0
## ... Procrustes: rmse 0.2213181  max resid 0.3503163
## Run 64 stress 0
## ... Procrustes: rmse 0.1501829  max resid 0.2294057
## Run 65 stress 0
## ... Procrustes: rmse 0.1411666  max resid 0.2546569
## Run 66 stress 0
## ... Procrustes: rmse 0.1464234  max resid 0.2116882
## Run 67 stress 0
## ... Procrustes: rmse 0.1652729  max resid 0.2477694
## Run 68 stress 9.870175e-05
## ... Procrustes: rmse 0.2505968  max resid 0.3328449
## Run 69 stress 0.07976986
## Run 70 stress 0
## ... Procrustes: rmse 0.194331  max resid 0.2432624
## Run 71 stress 6.941015e-05
## ... Procrustes: rmse 0.2130009  max resid 0.3004891
## Run 72 stress 7.615578e-05
## ... Procrustes: rmse 0.259831  max resid 0.34112
## Run 73 stress 0
## ... Procrustes: rmse 0.1647591  max resid 0.2388743
## Run 74 stress 0
## ... Procrustes: rmse 0.1644595  max resid 0.2847747
## Run 75 stress 0
## ... Procrustes: rmse 0.1906808  max resid 0.3100185
## Run 76 stress 0
## ... Procrustes: rmse 0.146477  max resid 0.2315368
## Run 77 stress 7.361458e-05
## ... Procrustes: rmse 0.2474006  max resid 0.3599023
## Run 78 stress 0
## ... Procrustes: rmse 0.1476474  max resid 0.2302322
## Run 79 stress 0
## ... Procrustes: rmse 0.1500008  max resid 0.1972427
## Run 80 stress 0
## ... Procrustes: rmse 0.2317812  max resid 0.3787597
## Run 81 stress 0
## ... Procrustes: rmse 0.2462261  max resid 0.3285394
## Run 82 stress 0
## ... Procrustes: rmse 0.1343457  max resid 0.1992015
## Run 83 stress 0
## ... Procrustes: rmse 0.1171339  max resid 0.2019657
## Run 84 stress 0
## ... Procrustes: rmse 0.1754114  max resid 0.255796
## Run 85 stress 0
## ... Procrustes: rmse 0.17915  max resid 0.2562237
## Run 86 stress 0
## ... Procrustes: rmse 0.2158695  max resid 0.2893261
## Run 87 stress 0
## ... Procrustes: rmse 0.1897326  max resid 0.3018936
## Run 88 stress 8.264709e-05
## ... Procrustes: rmse 0.2704232  max resid 0.3402092
## Run 89 stress 0
## ... Procrustes: rmse 0.1770887  max resid 0.2768628
## Run 90 stress 7.124833e-05
## ... Procrustes: rmse 0.2274275  max resid 0.3037865
## Run 91 stress 0
## ... Procrustes: rmse 0.2291196  max resid 0.3758455
## *** No convergence -- monoMDS stopping criteria:
##     90: stress < smin
##      1: stress ratio > sratmax
## [1] "No Convergence"






  OTU Abundance Per Sample






  OTU Abundance Per Treatment






  Pairwise Percent-ID Heatmap








  Taxonomy Result Visualization








  Phylogenetic Tree



This tree is a maximum likelihood tree made with IQTREE2 and the parameters you specified in the vampirus.config file. Also, this is an interactive tree, you can zoom in and hover on nodes to know the sequence ID. For a better visualization of this tree, you can find the *.treefile with bootstrap support values within the results directory and visualize using programs like FigTree or ITOL.